Study of complex genetic traits using a whole genome association strategy is becoming feasible as a result of haplotype and linkage disequilibrium maps being constructed by public and private groups together with highly mutliplexed single nucleotide polymorphism (SNP) genotyping platforms introduced by several companies. Once association is established for a handful of chromosomal regions by whole genome scans, narrowing down the individual regions to the point where mutation scanning of candidate genes is feasible requires the analysis of haplotypes of additional individuals. Because the highly multiplexed genotyping methods are not cost effective or efficient at this stage of the study, and haplotype prediction algorithms introduce errors that reduce the power of detecting association, it is desirable to develop new and robust technologies that determine haplotypes of large number of individuals efficiently and cost effectively. In this application, we propose to develop a molecular haplotyping method that is based on allele-specific tagging of SNPs on long PCR products with single molecule analysis. The final product is a method that can analyze 1,000 haplotypes per week and requires a set of instruments that an average laboratory can afford. To achieve this goal, we plan to (1) develop a robust allele-specific tagging method for long PCR products; (2) develop a method for efficient deposition of DNA molecules onto a glass surface; (3) develop accurate and robust approaches to analyze the DNA image for haplotype determination; (4) automate the DNA analysis process to increase the throughput of the molecular haplotyping method; (5) determine the haplotypes of the HapMap samples in a 500 kb ENCODE region on chromosome 7p. If successful, the method being developed in this project will provide a logical bridge between whole genome scan for association and candidate gene sequence analysis and facilitate the search for genetic factors associated with common genetic traits.